[gmx-users] Help with interpreting message for fatal error

Viveca Lindahl vivecalindahl at gmail.com
Sun Mar 11 15:30:57 CET 2018


I'm running a simulation of a periodic DNA molecule. After some time I get,
sometimes the following error message:


A list of missing interactions:
         Proper Dih. of   3917 missing      1

Molecule type 'DNA_chain_A'
the first 10 missing interactions, except for exclusions:
         Proper Dih. atoms  414  417  418  421 global   414   417   418

Program:     gmx mdrun, version 2018.1-dev-20180306-33093601f
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank:    0 (out of 32)

Fatal error:
1 of the 10381 bonded interactions could not be calculated because some
involved moved further apart than the multi-body cut-off distance (0.5465
or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 0
_pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32 2018]
PE RANK 0 exit signal Aborted
[NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
Application 12709959 exit codes: 134
Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
inblocks ~34261, outblocks ~55016
---> Reached end of run script.

How should I... proceed here? Is my system set up poorly, is it a bug in
mdrun? Suggestions appreciated.


More information about the gromacs.org_gmx-users mailing list